You are here

Genetic Analyses in Setaria

Project Summary

The main limiting factor to the use of cellulosic feedstock for bioenergy production through fermentation is recalcitrance to sugar release. This project is part of a larger effort by the BioEnergy Science Center to reduce recalcitrance in switchgrass. Using Setaria as a model for switchgrass, we aim to identify the genes that affect recalcitrance. A recombinant inbred line (RIL) population of a cross between the cultivated Setaria italica and its wild progenitor S. viridis will be analyzed for total lignin content, S/G lignin ratio and sugar release. Candidate genes underlying key QTL will be identified from known pathways (short term) or through map-based cloning (long-term), characterized for structural and functional variants, and their identify confirmed via genetic transformation. The knowledge gained in Setaria will be transferred to switchgrass to identify natural variants with reduced recalcitrance or to modify recalcitrance through genetic manipulation.

BioEnergy Science Website

Project Summary

Setaria viridis (L.) Beauv., green foxtail, is an inbreeding grass with a 500 Mb genome. This weed has successfully adapted to disturbed habitats in a large range of environmental conditions, including extensive pressure imposed by agricultural weed control that has led to the development of herbicide resistant genotypes. Green foxtail is therefore an ideal organism in which to study the effects of directional selection on genome evolution. Evolutionary genetic analyses in green foxtail have recently become feasible thanks to the development of genomic tools for Setaria, including an 8X genomic sequence of S. italica, the domesticated form of S. viridis, a 15X S. viridis sequence, and 1X sequence for an additional 10 S. viridis accessions. The project will use these resources plus a set of 200 lines of S. viridis, including both herbicide resistant and sensitive accessions. We plan to investigate the genomic effects of selection for mutations in three herbicide target genes, the nuclear-encoded chloroplast acetyl CoA carboxylase (ACCase) gene, the acetolactate synthase (ALS) gene and the α-tubulin gene, which are located on chromosomes VII, I and IX, respectively. Because whole-genome sequencing at a depth required for unambiguous SNP detection is too expensive, a genome-reduction strategy will be combined with Illumina sequencing. In addition, we will sequence the complete ACCase, ALS and α-tubulin genes. Using this methodology, haplotype diversity will be examined in all lines to assess (1) the diversity of green foxtail in the world and in North America; (2) the history and origin of green foxtail introductions into North America from Eurasia; (3) the nature of mutations that can give rise to target-site resistance; (4) whether resistance to each of the three classes of herbicides has originated multiple times or has spread across regions through seed dispersal and/or gene flow; and (5) the effects of selection for herbicide resistance on linkage disequilibrium surrounding the target genes. The results of this study will provide new insights on rapid evolution due to intense directional selection pressures.

Project Highlights

S. viridis accessions from North America group into three populations with considerable admixture between the three groups. Genetic diversity significantly correlates with the geographic origin and climate at the collection site. Overall linkage disequilibrium declines within 45 kb across the three subpopulations but extends over larger distances within subpopulations.